workflow fix; small cleanup

.github/workflows/AdEx.yml

@@ -29,7 +29,7 @@ jobs:
 
       - name: Install
         run: |
-          python3 -mvenv venv
+          python3 -m venv venv
           source venv/bin/activate
           pip install -r AdEx/requirements.txt
           cd arbor

.github/workflows/STDP.yml

@@ -29,7 +29,7 @@ jobs:
 
       - name: Install
         run: |
-          python3 -mvenv venv
+          python3 -m venv venv
           source venv/bin/activate
           pip install -r STDP/requirements.txt
           cd arbor

.github/workflows/homeostasis.yml

@@ -29,7 +29,7 @@ jobs:
 
       - name: Install
         run: |
-          python3 -mvenv venv
+          python3 -m venv venv
           source venv/bin/activate
           pip install -r spike_based_homeostasis/requirements.txt
           cd arbor

README.md

@@ -8,7 +8,7 @@ were ported and augmented in correspondence to neuro-theoretical
 investigations by the [Tetzlaff research group](https://tetzlab.com) at
 University of Göttingen.
 
-## Arbor implementations -- FIPPA output
+## Arbor implementations -- output of FIPPA
 
 * [Spike-timing-dependent plasticity (STDP)](STDP)
 * [Spike-based homeostasis](spike_based_homeostasis)

STDP/README.md

@@ -8,7 +8,7 @@ The implementation is validated against the Brian 2 simulator.
 
 # How to
 
-First, install Arbor. If you install from source, make sure `build-catalogue` from the Arbor
+First, install Arbor. If you install from source, make sure `arbor-build-catalogue` from the Arbor
 scripts directory is in `PATH`, or modify the `Makefile` accordingly.
 
 Next, if necessary, adapt `run_arbor.sh` and `run_brian2.sh` to your environment.

STDP/requirements.txt

@@ -2,3 +2,4 @@ numpy
 matplotlib
 brian2
 scipy
+sklearn

STDP/run_arbor.sh

@@ -13,6 +13,8 @@ variant="$1"
 # export PATH=$(readlink -f ~/local/bin):$PATH
 # export PYTHONPATH=$(readlink -f ~/local/lib/python3.8/site-packages):${PYTHONPATH-}
 # export LD_LIBRARY_PATH=$(readlink -f ~/local/lib):${LD_LIBRARY_PATH-}
+# or,
+# source set_arbor_env
 
 ./arbor_stdp_lif.py "$variant"
-./arbor_stdp_classical.py "$variant"
+./arbor_stdp_classical.py "$variant"

STDP/set_arbor_env

@@ -4,24 +4,24 @@
 
 # check if PATH exists and set environment variable accordingly
 if [[ ! -v PATH ]]; then
-	export PATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/bin)
+	export PATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/bin)
 else
-	export PATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/bin):$PATH
+	export PATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/bin):$PATH
 fi
 
 # check if LD_LIBRARY_PATH exists and set environment variable accordingly
 if [[ ! -v LD_LIBRARY_PATH ]]; then
-	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/lib)
+	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/lib)
 else
-	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/lib):$LD_LIBRARY_PATH
+	export LD_LIBRARY_PATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/lib):$LD_LIBRARY_PATH
 fi
 
 # check if PYTHONPATH exists and set environment variable accordingly
 if [[ ! -v PYTHONPATH ]]; then
-	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/lib/python3.8/site-packages) # or: .../python3.6/..., etc.
+	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/lib/python3.10/site-packages) # or: .../python3.8/..., etc.
 else
-	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd/lib/python3.8/site-packages):$PYTHONPATH # or: .../python3.6/..., etc.
+	export PYTHONPATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd/lib/python3.10/site-packages):$PYTHONPATH # or: .../python3.8/..., etc.
 fi
 
 # set CMAKE_PREFIX_PATH environment variable
-export CMAKE_PREFIX_PATH=$(readlink -f ~/arbor_v0.9.1dev-xd-bugfix-simd)
+export CMAKE_PREFIX_PATH=$(readlink -f ~/arbor_v0.9.1-dev-plastic_arbor_v1-simd)